Hi all
I am running RE tutorial in develpment version, but a question arise.
When is estimated the potential using cubic splines, how do you
specifed the number of knots ? in the tutorial they are 48.
<!-- function form for the potential (lj126 or ljg or cbspl)-->
<function>cbspl</function>
<cbspl>
<!-- no. of knots for cbspl function -->
<nknots>48</nknots>
Thanking in advance your help
Best Regards
Marc
Dr. Marc Segovia
CCBG-DETEMA
Facultad de Quimica
Universidad de la Republica
11800 Montevideo
Uruguay
On Fri, Nov 1, 2013 at 11:57 PM, Sikandar Mashayak <[email protected]>wrote:
> Hi Marc
>
> The option "nknots_cutoff" was earlier used in the settings.xml file to
> specify number of cubic B-spline knots near the cut off which should be
> forced to value 0.0 to ensure that CG potential smoothly goes to zero near
> the cut-off.
>
> Later, I decided to fix this nknots_cutoff = 4 because I think fixing 4
> knot values near the cut-off is sufficient in most of the cases and user
> should not worry about this number. Hence, instead of taking this number as
> an input from user, it is fixed in the source code.
>
> You should not get the error "property not found: nknots_cutoff" if you
> are using latest source code of votca-csg (i.e., revision >
> 681d33b7942b<http://code.google.com/p/votca/source/detail?r=681d33b7942bba2d3d213f4e321b17e0c6a00676&repo=csg>).
>
>
> So could you please check if you are correctly downloading the latest
> version and installing it. Because, I dont get the same error, when I test
> the water spce relative entropy tutorial with the latest development
> version of csg source code.
>
> You can check if you are using the latest version of votca-csg by running
> "csg_inverse -h" it will print out the version of votca-csg that you are
> using.
>
> Let us know if you face issues with updating and installing the latest
> development version of votca-csg.
>
> Thanks
> Sikandar
>
>
>
> On Fri, Nov 1, 2013 at 6:03 PM, Marc Segovia <[email protected]>wrote:
>
>> Good Night Everyone
>>
>> I am trying to run re tutorial with spce, but an error appear about
>> nknots_cutoff property, I update my dev version without sucess, any
>> suggestion ?
>>
>> Wishing a very good weekend and thanking in advance .
>>
>> Marc
>>
>> Dr. Marc Segovia
>> CCBG
>> Facultad de Quimica
>> Universidad de la Republica
>> 11800 Montevideo
>> Uruguay
>>
>> ~/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/step_000
>> Generating potential tables from the initial parameters
>> Running critical command 'csg_reupdate --gentable true --param-in-ext
>> param.new --options
>> /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/settings.xml'
>> an error occurred:
>> property not found: nknots_cutoff
>>
>> Callstack:
>> /home/marc/votca1.3/share/votca/scripts/inverse/inverse.sh - linenumber
>> 166
>> do_external - linenumber 171 in
>> /home/marc/votca1.3/share/votca/scripts/inverse/functions_common.sh
>> /home/marc/votca1.3/share/votca/scripts/inverse/prepare_re.sh -
>> linenumber 36
>> critical - linenumber 4 (see 'csg_call --cat function
>> critical')
>> die - linenumber 2 (see 'csg_call --cat function die')
>>
>> ################################################################################################################################################################
>> #
>> #
>> #
>> ERROR:
>> #
>> # critical: 'csg_reupdate --gentable true --param-in-ext param.new
>> --options
>> /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/settings.xml'
>> failed #
>> # For details see the logfile
>> /home/marc/votca1.3/csg-tutorials.votca-695b567ead5c/spce/re/inverse.log
>> #
>> #
>> #
>>
>> ################################################################################################################################################################
>> die: (called from 318) CSG_MASTER_PID is 31799
>> die: pids to kill: 31799 318
>>
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